Displaying Results with Streamlines After Masking

Hello MRtrix Experts!

My question is about displaying results with streamlines (3D image from template derived tractogram) following fixelcfestats with the -mask option.

Below is the result from my original FBA without a mask. After I ran fixelcfestats, I did fixel2tsf stats_fdc/fwe_pvalue.mif tracks_200k_sift.tck fdc_fwe_pvalue.tsf and was able to easily see my results in 3D after thresholding. Below is an image from my original analysis with my streamline picture on the left and the fixel plot on the right.

I decided I wanted to try and mask out areas of CSF, so I re-did fixelcfestats with the mask option. When I look at my fixel plot, my results don’t look much different (which I expected). However, when I do fixel2tsf and display streamlines, it also seems like it just “thins out” the tractogram, and is not thresholding it by significance. Everything is the same between these two analyses except for the -mask option.

Thank you very much for your time,

Hi Shannon,

I can’t envisage any software mechanism that could lead to a result like this. Unfortunately TSF files do not (yet) store provenance information, so we can’t check that; but it really needs to be verified that this is some sort of reproducible issue before we can pursue any further. Can you re-generate both TSF files, using the same commands in both cases, and still get the same results as shown in your posted screenshots? If so, you’ll probably need to provide adequate data for one of us to be able to reproduce ourselves.


Hi Rob,
Thank you so much for getting back. I re-ran fixelcfestats twice using all the same data: once using the mask option, one without the mask option. I then applied the same fixel2tsf function to both files, and I get the same “thinning out” streamline display for my mask results only. If you think the next best step is to provide you with all necessary files, could you please tell me the best way to get these to you?